Workflow

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Heatmaps

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QC plot

Statistics

If the workflow has been executed in cluster/cloud, runtimes include the waiting time in the queue.

Configuration

Configuration files
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samplemetadata: "metadata/samples.csv"
classifier_training_data: "refdata/human/classifier_training_data.h5"
reference_gc: refdata/human/reference_gc_grch37.csv

refdir: refdata/
thousand_genomes_snps: refdata/human/thousand_genomes_snps.tsv
ref_genome: refdata/human/GRCh37-lite.fa

mappability:
  local_path: refdata/human/wgEncodeCrgMapabilityAlign50mer.bigWig
  url: http://hgdownload-test.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/release3/wgEncodeCrgMapabilityAlign50mer.bigWig

schnapps:
  mincells: 5
  qualfilter: 0.0

# refdata/human/GRCh37-lite.gc.ws_500000.wig
#refdata/human/GRCh37-lite.map.ws_125_to_500000.wig

hmmcopy:
  bin_size: 200000
  gc_wig_file: hmmcopy_wigfiles/wigfiles/grch37/GRCh37-lite.gc.ws_200000.wig
  map_wig_file: hmmcopy_wigfiles/wigfiles/grch37/GRCh37-lite.map.ws_200000.wig
  ref_genome: refdata/human/GRCh37-lite.fa
  chromosomes:
  - '1'
  - '2'
  - '3'
  - '4'
  - '5'
  - '6'
  - '7'
  - '8'
  - '9'
  - '10'
  - '11'
  - '12'
  - '13'
  - '14'
  - '15'
  - '16'
  - '17'
  - '18'
  - '19'
  - '20'
  - '21'
  - '22'
  - X
  - Y
  docker:
    hmmcopy: hmmcopy:v0.0.6
    single_cell_pipeline: single_cell_pipeline:v0.6.41
  e: 0.999999
  eta: 50000
  exclude_list: refdata/human/repeats.satellite.regions
  g: 3
  good_cells:
  - - median_hmmcopy_reads_per_bin
    - ge
    - 50
  - - is_contaminated
    - in
    - - 'False'
      - 'false'
      - false
  igv_segs_quality_threshold: 0.75
  kappa: "100,100,700,100,25,25,25,25,25,25,25,25"
  lambda: 20
  m: "0,1,2,3,4,5,6,7,8,9,10,11"
  map_cutoff: 0.9
  memory:
    med: 6
  min_mqual: 20
  mu: "0,1,2,3,4,5,6,7,8,9,10,11"
  multipliers: "1,2,3,4,5,6"
  nu: 2.1
  num_states: 12
  s: 1
  smoothing_function: modal
  strength: 1000

infer_haps:
  chromosomes:
  - '1'
  - '2'
  - '3'
  - '4'
  - '5'
  - '6'
  - '7'
  - '8'
  - '9'
  - '10'
  - '11'
  - '12'
  - '13'
  - '14'
  - '15'
  - '16'
  - '17'
  - '18'
  - '19'
  - '20'
  - '21'
  - '22'
  - X
  - Y
  extract_seqdata:
    genome_fai_template: refdata/human/GRCh37-lite.fa.fai
    genome_fasta_template: refdata/human/GRCh37-lite.fa
  max_cores: null
  memory:
    high: 16
    low: 4
    med: 6
  ref_data_dir: refdata/human/

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